Rxivist logo

Tximeta: reference sequence checksums for provenance identification in RNA-seq

By Michael I. Love, Charlotte Soneson, Peter F. Hickey, Lisa K. Johnson, N. Tessa Pierce, Lori Shepherd, Martin Morgan, Rob Patro

Posted 25 Sep 2019
bioRxiv DOI: 10.1101/777888 (published DOI: 10.1371/journal.pcbi.1007664)

Correct annotation metadata is critical for reproducible and accurate RNA-seq analysis. When files are shared publicly or among collaborators with incorrect or missing annotation metadata, it becomes difficult or impossible to reproduce bioinformatic analyses from raw data. It also makes it more difficult to locate the transcriptomic features, such as transcripts or genes, in their proper genomic context, which is necessary for overlapping expression data with other datasets. We provide a solution in the form of an R/Bioconductor package tximeta that performs numerous annotation and metadata gathering tasks automatically on behalf of users during the import of transcript quantification files. The correct reference transcriptome is identified via a hashed checksum stored in the quantification output, and key transcript databases are downloaded and cached locally. The computational paradigm of automatically adding annotation metadata based on reference sequence checksums can greatly facilitate genomic workflows, by helping to reduce overhead during bioinformatic analyses, preventing costly bioinformatic mistakes, and promoting computational reproducibility. The tximeta package is available at https://bioconductor.org/packages/tximeta.

Download data

  • Downloaded 591 times
  • Download rankings, all-time:
    • Site-wide: 25,289 out of 89,138
    • In bioinformatics: 3,474 out of 8,414
  • Year to date:
    • Site-wide: 12,072 out of 89,138
  • Since beginning of last month:
    • Site-wide: 36,805 out of 89,138

Altmetric data

Downloads over time

Distribution of downloads per paper, site-wide


Sign up for the Rxivist weekly newsletter! (Click here for more details.)